ProCKSI

= Data Storage =

This page describes the design of the database that is/will be used in order to store all necessary pieces information that are obtained from the "stand-alone" ProCKSI ''core'' application (see [wiki:DataStandardisation]).

Database Design for the (static) Protein Multiverse
Image(ProteinMultiverseDataBase.png)

'''Explenation of the database design''': * There are multiple similarity comparison ''Methods'': e.g. USM, MaxCMO, DaliLite, ... * There are multiple similarity ''Measures'': e.g. Z-score, TM-score, Number of Alignments, ... * Some ''Methods'' produce ''Measures'' with the same name, but not necessarily the same meaning: e.g. DaliLite/Z, TMalign/Z, ...br
Thus, a ''!MethodMeasures'' relation is necessary.

• Each ''Method'' can have multiple (different) ''Parameters'': e.g. USM/Compressor, USM/Equation, ...
• Each ''Method'' can have multiple (different) ''!ParameterOptions'': USM/Compressor/bzip, USM/Compressor/gzip, ...
• A "!ParameterSet" is used to calculate the ''Similarity'' of ''!StructurePairs''. It is a collection of specific ''!ParameterSetOptions''. If a ''Method'' does not use any parameters, it is not included in the ''!ParameterSet'', but accessible via the ''!MethodMeasure'' relation.

• The ''!StructurePairs'' relation holds all possible combinations of ''Structures'', and a link to a further ''Results'' file in XML format. This file may contain results for multiple ''!StructurePairs'', e.g. alignments, matrices, etc.
• Each ''Structure'' is uniquely determined by its PDB code, model and chain. (Domains are not taken into accout yet.) The location of the PDB file is given and a link to a further ''Results'' file in XML format. This file may contain additional information for multiple ''Structures'', e.g. sequence, secondary structure, experimental resolution, ...

• Each ''Structure'' is extended by further classifiction information from ''CATH'' and ''SCOP''.

Extended Database Design for the (static) Protein Multiverse

Image(ProteinMultiverseDataBaseExt2.png)

This proposal for an extended database design for the (static) Protein Multiverse aims to include not only ''Comparisons'' but also ''Transformations'' and ''Compositions'' (following the latest development of the I/O specificaitions for the ProCKSI "stand-alone" ''core'' application): * A ''Transformation'' is a process that derives ONE (main) ''Result'' from ONE single input file.br
Example: The transformation of ''Structure'', ''Tree'', ''!SimilarityMatrix'', etc., using a certain ''Method'' with a certain ''!ParameterSet'', produces a contact map, a tree, ... * A ''Comparison'' is a process that derives ONE (main) ''Result'' from TWO input files. br
Example The comparison of ''Structures'', ''Trees'', etc., using a ''Method'' with a certain ''!ParameterSet'', produces a similarity value and an alignment * A ''Composition'' is a process that derive ONE (main) ''Result'' from SEVERAL input files that are grouped together into a ''DataSets''. br
Example The composition of ''!SimilarityMatrices'', ''Trees'', using a ''Method'' with a certain ''!ParameterSet'', produces a consensus similarity matrix, a consensus tree, ...

This design does not allow ''Datasets'' to comprise other files than ''Structures'' although some of the ''Results'' need to form a ''Dataset''.br
Example Contact maps that have been produces by a ''Transformation'' of ''Structures'' and that are available from within the ''Results'' need to form a ''Dataset'' in order to act as input for the ''Comparisons'' with the USM or MaxCMO ''Methods''.

Extended Database Design for (dynamic) Management of Experiments (ProCKSI)

This has not been modelled yet, but the database for the (static) Protein Multiverse was designed with the ProCKSI integration in mind.

Some remarks: * ''Experiments'' (formerly ''Requests'') apply "Methods" to "!DataSets" with a certain "!ParameterSet''. * ''Packages'' (formerly ''Jobs'') deal with a subset of a "!DataSet" and a subset of the requested ''Methods'', partitioning the the 3D problem space, and are calculated using the ProCKSI's "stand-alone" core application "in one go". If they are sent to a queuing system, they become a ''Job'' there. * It has to be discussed if there is still the need of a ''Tasks'' relation in the database, which have always been rather ''!RequestMethods''.